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Kojima M, Abe S, Furuta T, Hirata K, Yao X, Kobayashi A, Kobayashi R, Ueno T. High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization. Proc Natl Acad Sci U S A 2024; 121:e2322452121. [PMID: 38861600 PMCID: PMC11194560 DOI: 10.1073/pnas.2322452121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) play a crucial role in various biological phenomena, dynamically changing their conformations in response to external environmental cues. To gain a deeper understanding of these proteins, it is essential to identify the determinants that fix their structures at the atomic level. Here, we developed a pipeline for rapid crystal structure analysis of IDP using a cell-free protein crystallization (CFPC) method. Through this approach, we successfully demonstrated the determination of the structure of an IDP to uncover the key determinants that stabilize its conformation. Specifically, we focused on the 11-residue fragment of c-Myc, which forms an α-helix through dimerization with a binding partner protein. This fragment was strategically recombined with an in-cell crystallizing protein and was expressed in a cell-free system. The resulting crystal structures of the c-Myc fragment were successfully determined at a resolution of 1.92 Å and we confirmed that they are identical to the structures of the complex with the native binding partner protein. This indicates that the environment of the scaffold crystal can fix the structure of c-Myc. Significantly, these crystals were obtained directly from a small reaction mixture (30 µL) incubated for only 72 h. Analysis of eight crystal structures derived from 22 mutants revealed two hydrophobic residues as the key determinants responsible for stabilizing the α-helical structure. These findings underscore the power of our CFPC screening method as a valuable tool for determining the structures of challenging target proteins and elucidating the essential molecular interactions that govern their stability.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Kunio Hirata
- Synchrotron Radiation Life Science Instrumentation Unit, RIKEN/SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo679-5148, Japan
| | - Xinchen Yao
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Ayako Kobayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Ririko Kobayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
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2
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Schönherr R, Boger J, Lahey-Rudolph JM, Harms M, Kaiser J, Nachtschatt S, Wobbe M, Duden R, König P, Bourenkov G, Schneider TR, Redecke L. A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun 2024; 15:1709. [PMID: 38402242 PMCID: PMC10894269 DOI: 10.1038/s41467-024-45985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024] Open
Abstract
With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - J Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Hamburg, Germany
- X-ray technology lab, TH Lübeck - University of Applied Sciences Lübeck, Lübeck, Germany
| | - Mareike Harms
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | | | | | - Marla Wobbe
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Rainer Duden
- Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Peter König
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), University of Lübeck, German Center for Lung Research (DZL), Lübeck, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany.
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
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3
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Hamad M, AlKhamach DMH, Alsayadi LM, Sarhan SA, Saeed BQ, Sokovic M, Ben Hadda T, Soliman SSM. Alpha to Omicron (Variants of Concern): Mutation Journey, Vaccines, and Therapy. Viral Immunol 2023; 36:83-100. [PMID: 36695729 DOI: 10.1089/vim.2022.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initially emerged in December 2019 and has subsequently expanded globally, leading to the ongoing pandemic. The extensive spread of various SARS-CoV-2 variants possesses a serious public health threat. An extensive literature search along with deep analysis was performed to describe and evaluate the characteristics of SARS-CoV-2 variants of concern in relation to the effectiveness of the current vaccines and therapeutics. The obtained results showed that several significant mutations have evolved during the COVID-19 pandemic. The developed variants and their various structural mutations can compromise the effectiveness of several vaccines, escape the neutralizing antibodies, and limit the efficiency of available therapeutics. Furthermore, deep analysis of the available data enables the prediction of the future impact of virus mutations on the ongoing pandemic along with the selection of appropriate vaccines and therapeutics.
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Affiliation(s)
- Mohamad Hamad
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Dana M H AlKhamach
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | | | | | - Marina Sokovic
- Institute for Biological Research "Siniša Stanković," National Institute of the Republic of Serbia, University of Belgrade, Beograd, Serbia
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sameh S M Soliman
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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Kojima M, Abe S, Furuta T, Tran DP, Hirata K, Yamashita K, Hishikawa Y, Kitao A, Ueno T. Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein. Biomater Sci 2023; 11:1350-1357. [PMID: 36594419 DOI: 10.1039/d2bm01759h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein crystals can be utilized as porous scaffolds to capture exogenous molecules. Immobilization of target proteins using protein crystals is expected to facilitate X-ray structure analysis of proteins that are difficult to be crystallized. One of the advantages of scaffold-assisted structure determination is the analysis of metastable structures that are not observed in solution. However, efforts to fix target proteins within the pores of scaffold protein crystals have been limited due to the lack of strategies to control protein-protein interactions formed in the crystals. In this study, we analyze the metastable structure of the miniprotein, CLN025, which forms a β-hairpin structure in solution, using a polyhedra crystal (PhC), an in-cell protein crystal. CLN025 is successfully fixed within the PhC scaffold by replacing the original loop region. X-ray crystal structure analysis and molecular dynamics (MD) simulation reveal that CLN025 is fixed as a helical structure in a metastable state by non-covalent interactions in the scaffold crystal. These results indicate that modulation of intermolecular interactions can trap various protein conformations in the engineered PhC and provides a new strategy for scaffold-assisted structure determination.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Yuki Hishikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan. .,International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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Cell-free protein crystallization for nanocrystal structure determination. Sci Rep 2022; 12:16031. [PMID: 36192567 PMCID: PMC9530169 DOI: 10.1038/s41598-022-19681-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
In-cell protein crystallization (ICPC) has been investigated as a technique to support the advancement of structural biology because it does not require protein purification and a complicated crystallization process. However, only a few protein structures have been reported because these crystals formed incidentally in living cells and are insufficient in size and quality for structure analysis. Here, we have developed a cell-free protein crystallization (CFPC) method, which involves direct protein crystallization using cell-free protein synthesis. We have succeeded in crystallization and structure determination of nano-sized polyhedra crystal (PhC) at a high resolution of 1.80 Å. Furthermore, nanocrystals were synthesized at a reaction scale of only 20 μL using the dialysis method, enabling structural analysis at a resolution of 1.95 Å. To further demonstrate the potential of CFPC, we attempted to determine the structure of crystalline inclusion protein A (CipA), whose structure had not yet been determined. We added chemical reagents as a twinning inhibitor to the CFPC solution, which enabled us to determine the structure of CipA at 2.11 Å resolution. This technology greatly expands the high-throughput structure determination method of unstable, low-yield, fusion, and substrate-biding proteins that have been difficult to analyze with conventional methods.
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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Tetreau G, Andreeva EA, Banneville AS, De Zitter E, Colletier JP. Can (We Make) Bacillus thuringiensis Crystallize More Than Its Toxins? Toxins (Basel) 2021; 13:toxins13070441. [PMID: 34206749 PMCID: PMC8309801 DOI: 10.3390/toxins13070441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
The development of finely tuned and reliable crystallization processes to obtain crystalline formulations of proteins has received growing interest from different scientific fields, including toxinology and structural biology, as well as from industry, notably for biotechnological and medical applications. As a natural crystal-making bacterium, Bacillus thuringiensis (Bt) has evolved through millions of years to produce hundreds of highly structurally diverse pesticidal proteins as micrometer-sized crystals. The long-term stability of Bt protein crystals in aqueous environments and their specific and controlled dissolution are characteristics that are particularly sought after. In this article, we explore whether the crystallization machinery of Bt can be hijacked as a means to produce (micro)crystalline formulations of proteins for three different applications: (i) to develop new bioinsecticidal formulations based on rationally improved crystalline toxins, (ii) to functionalize crystals with specific characteristics for biotechnological and medical applications, and (iii) to produce microcrystals of custom proteins for structural biology. By developing the needs of these different fields to figure out if and how Bt could meet each specific requirement, we discuss the already published and/or patented attempts and provide guidelines for future investigations in some underexplored yet promising domains.
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Lahey-Rudolph JM, Schönherr R, Jeffries CM, Blanchet CE, Boger J, Ferreira Ramos AS, Riekehr WM, Triandafillidis DP, Valmas A, Margiolaki I, Svergun D, Redecke L. Rapid screening of in cellulo grown protein crystals via a small-angle X-ray scattering/X-ray powder diffraction synergistic approach. J Appl Crystallogr 2020; 53:1169-1180. [PMID: 33117106 PMCID: PMC7534541 DOI: 10.1107/s1600576720010687] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/03/2020] [Indexed: 11/24/2022] Open
Abstract
Crystallization of recombinant proteins in living cells is an exciting new approach for structural biology that provides an alternative to the time-consuming optimization of protein purification and extensive crystal screening steps. Exploiting the potential of this approach requires a more detailed understanding of the cellular processes involved and versatile screening strategies for crystals in a cell culture. Particularly if the target protein forms crystalline structures of unknown morphology only in a small fraction of cells, their detection by applying standard visualization techniques can be time consuming and difficult owing to the environmental challenges imposed by the living cells. In this study, a high-brilliance and low-background bioSAXS beamline is employed for rapid and sensitive detection of protein microcrystals grown within insect cells. On the basis of the presence of Bragg peaks in the recorded small-angle X-ray scattering profiles, it is possible to assess within seconds whether a cell culture contains microcrystals, even in a small percentage of cells. Since such information cannot be obtained by other established detection methods in this time frame, this screening approach has the potential to overcome one of the bottlenecks of intracellular crystal detection. Moreover, the association of the Bragg peak positions in the scattering curves with the unit-cell composition of the protein crystals raises the possibility of investigating the impact of environmental conditions on the crystal structure of the intracellular protein crystals. This information provides valuable insights helping to further understand the in cellulo crystallization process.
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Affiliation(s)
- Janine Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Clément E. Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
| | | | - Winnie Maria Riekehr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
| | | | - Alexandros Valmas
- Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, Patras GR-26500, Greece
| | - Irene Margiolaki
- Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, Patras GR-26500, Greece
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
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